[ome-users] Bioformats works only outside OME (more data)

Thu Jan 17 19:02:29 GMT 2008

Hi again,

It looks like I spoke too soon about the new loci_tools.jar not being
able to stitch files. Upon further investigation, it seems to be
working fine. I think my problem before was that OME's Perl Bio-Rad
PIC reader was overriding Bio-Formats on my system at the time, so it
read my test dataset as 12 separate Images, rather than a single
Image.

Once again, you can find the updated loci_tools.jar here:
http://skyking.microscopy.wisc.edu/curtis/jar/loci_tools.jar

Please let me know if it doesn't work for you.

-Curtis

On Jan 15, 2008 1:56 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> Hi Mario, Linda, and everyone,
>
> I isolated the most serious problem to a change we made on December
> 11th (r3465). I have fixed several problems including that one, and
> placed a working loci_tools.jar you can try here:
>
> http://skyking.microscopy.wisc.edu/curtis/jar/loci_tools.jar
>
> Just overwrite the one in /OME/java with that one, and hopefully
> things will work better.
>
> We will try to make another official release of the library soon, to
> minimize the number of new OME installations that are affected by this
> problem.
>
> Please note what Ilya and I said earlier about rearranging the order
> of importers, though -- if you don't, Bio-Formats will not be used for
> certain formats including Deltavision, BMP, Molecular Dynamics GEL,
> Metamorph STK, DICOM, TIFF & OME-TIFF, Bio-Rad PIC, and Zeiss LSM.
>
> Also please note that there are undoubtably still some (hopefully more
> minor) bugs -- in particular, the file stitching is not working
> properly. This means you cannot yet import a single Image distributed
> across multiple numbered files (e.g., data1.tiff, data2.tiff,
> data3.tiff, etc.). This functionality used to work, so is probably
> just a matter of me fixing more bugs in the Bio-Formats file stitching
> code somewhere.
>
> Linda, to revisit your earlier question about metadata: this updated
> version of Bio-Formats should properly include all the original
> key/value metadata pairs in the OME import. To see these values, after
> importing the Image, click the Image thumbnail to bring up the Image
> details screen. Among other things, you'll see a "Module executions"
> box on the top right. The first link in that box should say "Image
> import" -- click it, and you'll receive a detailed list of
> information, including the key/value pairs in their original format
> beneath a section labeled "OriginalMetadata." Please let me know if it
> doesn't work for you.
>
> Lastly, in the process of debugging, I regenerated several old
> versions of loci_tools.jar. I placed them online, in case anyone else
> wants them to do their own testing:
>
> http://skyking.microscopy.wisc.edu/curtis/archive/
>
> Please let me know if you continue to have trouble, or have any
> additional questions.
>
> -Curtis
>
>
> On Jan 11, 2008 12:22 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> > Hi Mario & Ilya,
> >
> > As I said yesterday, there is a critical problem with the latest
> > Bio-Formats and OME server. I was afraid of this, as I have honestly
> > been too neglectful of testing with OME server recently. I am looking
> > into the problem today, and hope to have a solution as soon as
> > possible. In the meantime, Ilya, if you have a working version of
> > loci_tools.jar that you could post online somewhere temporarily for
> > people to use, that would be really helpful. Otherwise I can try
> > building a few of the old versions until I find one that works well.
> >
> > My sincerest apologies to Mario, Linda and any others who have been
> > struggling with the Bio-Formats/OME connectivity.
> >
> > -Curtis
> >
> >
> > On Jan 11, 2008 9:08 AM, Ilya Goldberg <igg at nih.gov> wrote:
> > > It seems more and more people are struggling with OME server's over-
> > > riding the new and better bioformats with its old and deprecated
> > > importers.
> > > See Curits's earlier post about re-arranging the importer priority to
> > > either eliminate OME's importers altogether, or move bioformats up in
> > > the priority list.
> > > We will make these changes permanent in future releases so that BF
> > > takes priority over everything else.
> > >
> > > There may be other problems with the connection, but in the default
> > > configuration, OME's importers will over-ride TIFF, LSM, and STK.
> > > They should still import them, but apparently there are potentially
> > > other issues with these files, and BF does a better job.  LIFF and
> > > LIF should have been delegated to BF, because there are no "native"
> > > importers for these.  Which makes me think there may be an unrelated
> > > problem with the BF setup.
> > >
> > > -Ilya
> > >
> > >
> > > On Jan 11, 2008, at 6:31 AM, Mario Valle wrote:
> > >
> > > > Continuing investigation I have found:
> > > >
> > > > - From the OME web interface I can import only TIFF files. No
> > > > error, nothing, only
> > > > "unrecognized format"
> > > >
> > > > - From the command line: ome import -d "dataset" image
> > > >   I can import TIFF, STK, ie. everything except formats supported
> > > > by the bioformats
> > > >   library.
> > > >
> > > > So seems there are two problems:
> > > >   1) the bioformats library not found
> > > >   2) the web server accessing only a minimal subset of the import
> > > > functionality.
> > > >
> > > > Help!
> > > >       mario
> > > >
> > > >
> > > > Mario Valle wrote:
> > > >> I'm still stuck at the image importing step...
> > > >>
> > > >> 1) Moved to OME 2.6.1 on Mac (here I'm administrator, so I can
> > > >> experiment)
> > > >> 2) installed latest loci_tools.jar under /OME/java
> > > >> 3) downloaded bftools, unpacked and added the same loci_tools.jar
> > > >> ar OME in the resulting
> > > >> directory
> > > >> 3) tried bfview with TIFF, LIF, LSM, STK, LIFF files. Everything
> > > >> works. Only TIFF with
> > > >> character encoding Mac cannot be visualized, but this is another
> > > >> problem.
> > > >> 3) tried to import the same files in OME, only the tiff files are
> > > >> imported.
> > > >> Seems like OME is using some old import method, but no other copy
> > > >> of loci_tools.jar is
> > > >> anywhere on the machine.
> > > >> Help!
> > > >>      mario
> > > >>
> > > >>
> > > >
> > > > --
> > > > Ing. Mario Valle
> > > > Visualization Group                              | http://
> > > > www.cscs.ch/~mvalle
> > > > Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
> > > > 610.82.60
> > > > v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
> > > > 610.82.82
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> > > >
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